I think part of the reason people dislike the idea that Joss was 'pandering' to the slash fans, aside from 1) it devaluing their slashy squee, and 2) it insulting Joss, is 3) the use of the word 'pander' and similar phrases.
1) and 2) are possible and probable [not entirely objective] reasons for people to disagree with the position that there's something to be annoyed with in Joss' comments, and I'm sure a lot of people are motivated by that, but 3)....
The implication that Joss is "pandering" to the slash fans by saying things like 'does anybody honestly think they never fucked' (I paraphrase, of course) does insult Joss, and some people care to defend his thoughts and contributions to the show and gayitude at large, and some don't, but it also carries an implication of insulting the intelligence of those people who are squeeing. Being pandered to implies that the squee-ers are falling for something, that they're not critical enough fans, that they've been hoodwinked, that they care more about The Gay than they do the quality of the show, or more about the Ho-Yay fix than they do about what the show does for gays in the real world, etc. etc. etc.
I'm not saying that's the intention of those using 'pander' and similar phrases; I think in reading people's opinions on the subject that it's not, that they're annoyed with Joss and somewhat with the writers -- but from the other end of the stick, that's the attached implication, whether intended or not. That is, if I agree with FanX and FanY that Joss threw jokey ho-yay into the series, and explicit commentary only into the DVDs after the series was over, because he was trying to suck up to the fans once it couldn't possibly hurt him, then I tacitly agree with the idea that I as a squee-er was one of those fans who was allowing myself to be sucked-up to. I'm not fond of that idea, and I'd hazard a guess that a lot of other people aren't as well, even if they've not put it together that it's part of what's annoying them.
(This is aside from my opinion that on a completely civil discussion level, I think the argument for Joss sucking up to fandom in this case just doesn't make sense, and the external reasons for not having explicit male hoyay with main characters do make sense. But that argument's been made already and I don't have much to add to it. I'm just saying, this is my analysis of (one reason) why I think people are being so passionate about the subject -- because it feels like a challenge of their own credulity/intelligence/etc.)